To answer my own question, the bit that was causing the problem was, of course, 
the duplicated Verb, not the duplicated Extension. The Verb is stored under the 
ProgId, not under the extension, despite the way things are laid out in Wix and 
therefore there can only be one Verb per ProgId. The following code achieves 
what I was hoping for:

      <Directory Id="ProgramFilesFolder" SourceName="program files" 
ShortSourceName="PROGRA~1">
        <Directory Id="APPLICATIONFOLDER" Name="MyApp" 
ShortName="MyAppShortName" DiskId="1">
          <Component Id="MainApplication" Guid="MyGuid1">
            ...
            <ProgId Id="MyApp.MyDocType" Description="[ProductName] Document" 
Icon="ID_MyGuid2" IconIndex="1">
              <Extension Id="wpl">
                <Verb Id="Open" Command="Open" TargetFile="ID_MyGuid3" 
Argument="/dde" />
              </Extension>
              <Extension Id="wow-playlist" />
            </ProgId>


The following code causes 
MyApp.wxs(MyLineNo) : error LGHT0130 : The primary key 
'regCEECC3C927D10BCB192BEE13F4F46715' is duplicated in table 'Registry'.  
Please remove one of the entries or rename a part of the primary key to avoid 
the collision.


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